fix: repair NodeNorm status test and refresh Babel expectations - #47
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fix: repair NodeNorm status test and refresh Babel expectations#47SkyeAv wants to merge 2 commits into
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The NodeNorm `/status` endpoint does not report `babel_version` or `babel_version_url` (that compendia metadata is exposed by the NameRes `/status` endpoint, whose test still passes). Asserting those keys on NodeNorm raised `KeyError: 'babel_version'` and failed CI. Assert only the fields NodeNorm actually returns: `status` and the underlying Redis database counts.
Two NodeNorm normalization examples had drifted from the current NCATSTranslator/Babel compendia and failed CI: - UMLS:C0004096 (asthma): preferred CURIE MONDO:0004979 -> MONDO:0100470, label 'asthma' -> 'Asthma'. - DRUGBANK:DB00083 (botulinum toxin type A): preferred CURIE UMLS:C0006050 -> DRUGBANK:DB00083, label 'Dysport' -> 'Botulinum toxin type A', category biolink:Protein -> biolink:ChemicalEntity. Also document at EXAMPLE_QUERIES that these expectations track the live Babel-backed NodeNorm service and may need a periodic refresh.
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Fixes the four failing
tests/test_nodenorm.pychecks that were red onmainand blocking unrelated PRs (e.g. #45). All four failures trace back to the live Translator services: the NodeNorm/statusendpoint never exposedbabel_version, and the Babel-backed compendia have drifted the preferred CURIEs, labels, and categories for two example queries.NodeNorm status test
babel_version/babel_version_urlassertions fromtest_nodenorm_status. Unlike NameRes (name-lookup.ci.transltr.io/status), the NodeNorm/statusresponse only reportsstatusanddatabases; asserting those keys raisedKeyError: 'babel_version'. The NameRes status test still assertsbabel_versionand continues to pass.status['status'] == 'running'anddatabases['eq_id_to_id_db']['count'] > 650_000_000.Normalization expectations
UMLS:C0004096(asthma): preferred CURIEMONDO:0004979→MONDO:0100470, labelasthma→Asthma.DRUGBANK:DB00083(botulinum toxin type A): preferred CURIEUMLS:C0006050→DRUGBANK:DB00083, labelDysport→Botulinum toxin type A, categorybiolink:Protein→biolink:ChemicalEntity.Design
EXAMPLE_QUERIESpins exact preferred CURIEs/labels/categories to the live Babel-backed NodeNorm, so these will drift again on the next compendia release. A comment now documents this so the next refresh is obvious. Relaxing to shape-only assertions would lose the characterization coverage these tests provide, so the pinned values were refreshed instead.tests/test_nodenorm.pyis touched;TCT/node_normalizer.pyand the NameRes tests are unchanged.Testing
uv run pytest tests/test_nodenorm.py --no-cov -q→11 passed in 17.04suv run pytest tests/ --no-cov -q→47 passed, 1 skipped in 34.47suv run ruff check tests/test_nodenorm.py→All checks passed!nodenorm.transltr.io/get_normalized_nodes) forUMLS:C0004096andDRUGBANK:DB00083.